Contacts of the helix formed by residues 410 - 425 (chain B) in PDB entry 2Z1Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ILE* 4.2 26.9 - - + +
67B THR* 3.4 30.1 - - - -
68B GLU* 2.8 29.1 + - - +
337B PHE* 4.4 1.3 - - - -
409B GLY* 1.3 75.4 - - - -
411B ARG* 1.3 67.5 + - - +
412B GLU* 3.2 7.6 - - + +
413B ASN* 3.1 36.0 + - + +
414B ILE* 3.3 11.3 + - - +
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Residues in contact with ARG 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B PHE* 3.3 64.0 + - + +
340B GLU* 3.4 28.5 - - - +
341B ASN* 2.6 21.9 + - - -
344B ILE* 3.8 21.4 - - - +
410B HIS* 1.3 73.0 - - - +
412B GLU* 1.3 63.6 + - - +
414B ILE* 3.0 5.5 + - - +
415B LEU* 3.0 43.5 + - + +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B HIS* 3.2 5.5 - - + +
411B ARG* 1.3 78.1 - - - +
413B ASN* 1.3 56.8 + - - +
415B LEU* 3.4 19.5 + - - +
416B GLU* 2.8 51.4 + - + +
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Residues in contact with ASN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 3.5 38.6 - - + +
61B LEU* 5.9 0.4 - - + -
409B GLY* 4.9 3.9 - - - -
410B HIS* 3.1 37.7 + - - +
412B GLU* 1.3 81.8 - - - +
414B ILE* 1.3 60.5 + - + +
416B GLU* 4.0 2.0 - - - +
417B ALA* 3.1 27.4 + - - +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 3.9 23.6 - - + -
341B ASN* 3.6 46.4 - - + +
344B ILE* 4.1 20.6 - - + -
345B ILE* 4.1 12.3 - - + -
407B ALA* 3.8 24.9 - - - +
409B GLY* 3.9 15.5 - - - +
410B HIS 3.3 13.5 - - - +
411B ARG 3.0 6.8 + - - +
413B ASN* 1.3 75.0 - - + +
415B LEU* 1.3 57.3 + - - +
417B ALA* 3.2 6.0 + - - +
418B CYS* 2.9 38.9 + - - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ILE* 4.2 28.7 - - + -
411B ARG* 3.0 36.1 + - + +
412B GLU* 3.5 26.7 - - - +
414B ILE* 1.3 76.3 - - - +
416B GLU* 1.3 56.2 + - - +
418B CYS* 3.1 7.3 + - + +
419B ARG* 3.0 27.5 + - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 4.0 13.7 - - + -
412B GLU* 2.8 29.2 + - + +
413B ASN* 4.0 4.9 - - - +
415B LEU* 1.3 74.2 - - - +
417B ALA* 1.3 65.0 + - - +
419B ARG* 3.1 36.8 + - - +
420B ARG* 2.8 55.3 + - - +
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 4.2 11.1 - - + +
61B LEU* 3.9 24.7 - - + -
387B VAL* 4.1 18.2 - - + -
413B ASN 3.1 20.2 + - - +
414B ILE 3.2 5.1 + - - +
416B GLU* 1.3 76.1 - - - +
418B CYS* 1.3 56.8 + - - +
420B ARG* 3.3 10.3 + - - +
421B PHE* 3.0 35.5 + - + -
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Residues in contact with CYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ILE* 4.0 16.4 - - + -
345B ILE* 4.0 22.7 - - - -
348B THR* 3.4 36.4 + - + -
414B ILE 2.9 22.2 + - - +
415B LEU* 3.1 7.8 + - + +
417B ALA* 1.3 74.7 - - - +
419B ARG* 1.3 66.7 + - - +
420B ARG 3.1 0.9 - - - -
421B PHE* 3.0 23.8 + - - +
422B LYS* 3.4 19.9 + - - +
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B LEU 3.0 14.5 + - - +
416B GLU* 3.1 43.6 + - - +
418B CYS* 1.3 74.9 - - - +
420B ARG* 1.3 75.2 + - - +
421B PHE 3.1 1.6 + - - -
422B LYS* 3.2 22.1 + - + +
423B GLN* 3.3 55.0 + - - +
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Residues in contact with ARG 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLN* 2.8 40.8 + - - +
59B ILE* 4.1 15.8 - - - +
385B THR* 2.7 44.7 + - - +
386B HIS* 3.5 17.6 + - - +
387B VAL* 4.2 6.8 - - + +
416B GLU* 2.8 51.5 + - - +
417B ALA* 3.4 10.8 - - - +
418B CYS 3.1 0.6 - - - -
419B ARG* 1.3 90.4 - - - +
421B PHE* 1.3 60.6 + - - +
423B GLN* 3.5 10.6 - - + +
424B LEU* 3.4 19.8 + - - +
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 4.4 13.5 - - + -
345B ILE* 5.4 0.9 - - + -
348B THR* 4.4 6.5 - - - +
349B PHE* 3.7 37.7 - + + -
352B LEU* 4.2 15.3 - - + -
381B ILE* 4.3 19.1 - - + -
385B THR* 4.6 6.7 - - + -
387B VAL* 3.8 40.8 - - + -
389B THR* 4.9 5.8 - - + -
405B VAL* 4.7 7.0 - - + -
417B ALA* 3.0 27.4 + - + -
418B CYS* 3.0 20.1 + - - +
420B ARG* 1.3 76.6 - - - +
422B LYS* 1.3 61.2 + - - +
424B LEU* 3.3 8.1 + - - +
425B TYR* 2.9 36.5 + + + +
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B THR* 3.8 33.1 - - - +
351B SER* 4.5 8.5 - - - +
352B LEU* 4.0 23.9 - - + +
418B CYS* 3.6 13.8 - - - +
419B ARG* 3.5 14.5 - - + +
421B PHE* 1.3 72.5 - - - +
423B GLN* 1.3 73.4 + - - +
425B TYR 3.1 20.3 + - - +
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Residues in contact with GLN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ARG* 3.5 43.9 + - - +
420B ARG* 3.5 14.1 - - + +
422B LYS* 1.3 77.9 - - - +
424B LEU* 1.3 62.9 + - - +
425B TYR 3.3 1.9 + - - +
426B LYS 5.7 1.0 - - - -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B GLU* 4.9 4.5 - - + +
381B ILE* 4.2 11.2 - - + -
384B LYS* 4.1 37.7 - - + +
385B THR* 3.4 22.7 - - + -
420B ARG 3.4 10.1 + - - +
421B PHE* 3.3 10.9 + - - +
422B LYS 3.2 0.6 - - - -
423B GLN* 1.3 80.7 - - - +
425B TYR* 1.3 111.4 + - + +
426B LYS* 4.4 1.7 + - - -
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Residues in contact with TYR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B PHE* 4.6 12.8 - + - -
352B LEU* 3.6 27.6 - - + +
354B TYR* 2.8 29.8 - + + +
369B PHE* 3.8 25.6 - + - -
372B GLN* 5.4 3.8 + - - -
377B VAL* 4.2 4.9 + - - +
380B GLU* 4.2 16.5 + - + +
381B ILE* 3.4 28.3 - - + +
421B PHE* 2.9 27.4 + + - +
422B LYS 3.1 13.7 + - - +
423B GLN 4.3 0.9 - - - +
424B LEU* 1.3 109.0 - - + +
426B LYS* 1.4 66.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il